Biology subjects

Wu, F.

Publications and source records attributed to Wu, F..

At least 163 records · Page 9Linked to original sources

bioRxiv2021

Structural insights into hormone recognition by the human glucose-dependent insulinotropic polypeptide receptor

Glucose-dependent insulinotropic polypeptide (GIP) is a peptide hormone that exerts crucial metabolic functions by binding and activating its cognate receptor, GIPR. As an important therapeutic target, GIPR has been subjected to intensive structural studies without success. Here, we report the cryo-EM structure of the human GIPR in complex with GIP and a Gs heterotrimer at a global resolution of 2.9 [A]. GIP adopts a single straight helix with its N terminus dipped into the receptor transmembrane domain (TMD), while the C-terminus is closely associated with the extracellular domain and extracellular loop 1. GIPR employs conserved residues in the lower half of the TMD pocket to recognize the common segments shared by GIP homologous peptides, while uses non-conserved residues in the upper half of the TMD pocket to interact with residues specific for GIP. These results provide a structural framework of hormone recognition and GIPR activation.

molecular biology↗

bioRxiv2021

The plant immune receptors NRG1.1 and ADR1 are calcium influx channels

Plant nucleotide-binding leucine-rich repeat receptors (NLRs) regulate immunity and cell death. RPW8 domain-containing "helper" NLRs (RNLs) are required by many "sensor" NLRs. Our crystal structure of the RNL N REQUIREMENT GENE 1.1 (NRG1.1) N-terminal signaling domain resembled that of the resting state plant resistosome-forming HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) and the animal MIXED-LINEAGE KINASE-LIKE (MLKL) cation channel. Active NRG1.1 oligomerized, was enriched in plasma membrane puncta and conferred cytoplasmic Ca2+ influx in plant and human HeLa cells. NRG1.1-dependent Ca2+ influx and cell death were sensitive to Ca2+ channel blockers. Ca2+ influx and cell death mediated by NRG1.1 and ACTIVATED DISEASE RESISTANCE 1 (ADR1), another RNL, required conserved negatively charged N-terminal residues. Thus, RNLs apparently form influx channels to directly regulate cytoplasmic [Ca2+] and consequent cell death. One Sentence SummaryA specific class of plant immune receptors function as calcium-permeable channels upon activation to induce cell death.

plant biology↗

bioRxiv2021

Neuromodulation of Behavioral Specialization: Tachykinin Signaling Inhibits Task-Specific Behavioral Responsiveness in Honeybee Workers

Behavioral specialization is key to the success of social insects and often compartmentalized among colony members leading to division of labor. Response thresholds to task-specific stimuli proximally regulate behavioral specialization but their neurobiological regulation is not understood. Here, we show that response thresholds to task-relevant stimuli correspond to the specialization of three behavioral phenotypes of honeybee workers. Quantitative neuropeptidome comparisons suggest two tachykinin-related peptides (TRP2 and TRP3) as candidates for the modification of these response thresholds. Based on our characterization of their receptor binding and downstream signaling, we then confirm the functional role of tachykinins: TRP2 injection and RNAi cause consistent, opposite effects on responsiveness to task-specific stimuli of each behaviorally specialized phenotype but not to stimuli that are unrelated to their tasks. Thus, our study demonstrates that TRP-signaling regulates the degree of task-specific responsiveness of specialized honeybee workers and may control the context-specificity of behavior in animals more generally.

evolutionary biology↗

bioRxiv2021

High-throughput tandem-microwell assay for ammonia repositions FDA-Approved drugs to Helicobacter pylori infection

To date, little attempt has been made to develop new treatments for Helicobacter pylori (H. pylori), although the community is aware of the shortage of treatments for H. pylori. In this study, we developed a 192-tandem-microwell-based high-throughput-assay for ammonia that is a known virulence factor of H. pylori and a product of urease. We could identify few drugs, i.e. panobinostat, dacinostat, ebselen, captan and disulfiram, to potently inhibit the activity of ureases from bacterial or plant species. These inhibitors suppress the activity of urease via substrate-competitive or covalent-allosteric mechanism, but all except captan prevent the antibiotic-resistant H. pylori strain from infecting human gastric cells, with a more pronounced effect than acetohydroxamic acid, a well-known urease inhibitor and clinically used drug for the treatment of bacterial infection. This study offers several bases for the development of new treatments for urease-containing pathogens and to study the mechanism responsible for the regulation of urease activity.

biochemistry↗

bioRxiv2020

Deep Template-based Protein Structure Prediction

MotivationTBM (template-based modeling) is a popular method for protein structure prediction. When very good templates are not available, it is challenging to identify the best templates, build accurate sequence-template alignments and construct 3D models from alignments. ResultsThis paper presents a new method NDThreader (New Deep-learning Threader) to address the challenges of TBM. DNThreader first employs DRNF (deep convolutional residual neural fields), which is an integration of deep ResNet (convolutional residue neural networks) and CRF (conditional random fields), to align a query protein to templates without using any distance information. Then NDThreader uses ADMM (alternating direction method of multipliers) and DRNF to further improve sequence-template alignments by making use of predicted distance potential. Finally NDThreader builds 3D models from a sequence-template alignment by feeding it and sequence co-evolution information into a deep ResNet to predict inter-atom distance distribution, which is then fed into PyRosetta for 3D model construction. Our experimental results on the CASP13 and CAMEO data show that our methods outperform existing ones such as CNFpred, HHpred, DeepThreader and CEthreader. NDThreader was blindly tested in CASP14 as a part of RaptorX server, which obtained the best GDT score among all CASP14 servers on the 58 TBM targets. Availability and Implementationavailable as a part of web server at http://raptorx.uchicago.edu Contactjinboxu@gmail.com Supplementary InformationSupplementary data are available online.

bioinformatics↗

bioRxiv2020

Zfp36l1 and Zfp36l2 balances proliferation and differentiation in the developing retina

Both transcriptional and post-transcriptional regulation of gene expression play significant roles in diverse biological processes, but little is known about how post-transcriptional regulation impacts retinal development. Here we report our study of the function of two members of the TTP (tristetraprolin) mRNA binding protein family, Zfp36l1 and Zfp36l2, in the developing retina. TTP proteins are highly conserved CCCH zinc finger proteins, which carry out their functions by promoting target mRNA decay and modulating translation. We found that Zfp36l1 and Zfp36l2 were expressed in retinal progenitor cells (RPCs) during development and Muller glial cells and photoreceptors in the mature retina. Our analysis of the mutant retinas showed that, whereas the single knockout retinas were largely normal, the double knockout (DKO) retina showed decreased RPC proliferation and increased differentiation of multiple retinal cell types. RNA-seq analysis confirmed the imbalance of proliferation and differentiation in the DKO retina. Gene ontology and in silico target gene analysis indicates that Zfp36l1 and Zfp36l2 exert their function by directly regulating multiple classes of proteins, including components of multiple signaling pathways such as the sonic hedgehog pathway and the Notch pathway, cell cycle regulators, and most interestingly transcription factors directly involved in retinal differentiation. These results reveal a new tier of gene regulation controlling retinal development.

developmental biology↗

bioRxiv2020

Extensive MET alterations confer clinical response to MET inhibitors in gliomas

Activating alterations of the MET gene are well-characterized oncogenic drivers, and MET inhibitors could successfully treat several tumor types with MET alterations, including gliomas with PTPRZ1-MET fusion. However, the full diversity and prevalence of MET alterations in gliomas are still lacking to accurately identify a subset of patients likely to benefit from MET inhibitor treatment. Here, we interrogated genomic profiles of 1,351 gliomas, and further identify 60 cases harboring MET alterations, including MET fusions and various MET exon skipping events. MET RNA alterations, but not MET amplification, are highly enriched in the secondary glioblastomas (sGBM) with significantly worse prognosis. Further molecular analysis has shown that MET RNA alterations acting an additive effects of MET overexpression are induced in the course of glioma evolution. In vitro and clinical studies indicate cells and patients harboring MET alterations have better response to MET inhibitors. Collectively, these data suggest that a subgroup of gliomas harboring MET alterations likely to have benefit from MET-targeted therapy.

neuroscience↗

bioRxiv2020

Expression analysis of photosynthesis-related genes in albino Artocarpus heterophyllus seedlings leaves

Albino Artocarpus heterophyllus Seedlings (AAS) were found in the preliminary investigation by our group and were used as materials for researching. The phenotype of AAS leaves were observed and measured. In parallel, the photosynthetic physiological parameters were determined under different photosynthetically active radiations (PAR). The results suggested that the length, width, area and thickness of AAS leaves were less than normal seedings. Likewise, the net photosynthetic rate, intercellular CO2 concentration, stomatal conductance and transpiration rate of AAS leaves were not susceptible to PAR in contrast to normal individuals. Furthermore, the transcriptome sequencing technology was performed to clarify the expression of genes related to photosynthesis. It is as expected that numerous down-regulated genes were found in the synthesis of photosynthetic pigments, as well as the pathways of photosynthesis - antenna proteins, photoreaction and carbon fixation reaction of AAS leaves. Compared to other albino plants, AAS have a longer life span and more stable phenotypic traits with larger leaves, which could provide ideal materials for investigating photosynthesis of woody plants.

physiology↗

bioRxiv2020

High-throughput whole-brain mapping of rhesus monkey at micron resolution

Whole-brain mesoscale mapping of primates has been hindered by large brain size and the relatively low throughput of available microscopy methods. Here, we present an integrative approach that combines primate-optimized tissue sectioning and clearing with ultrahigh-speed, large-scale, volumetric fluorescence microscopy, capable of completing whole-brain imaging of a rhesus monkey at 1 {micro}m x 1 {micro}m x 2.5 {micro}m voxel resolution within 100 hours. A progressive strategy is developed for high-efficiency, long-range tracing of individual axonal fibers through the dataset of hundreds of terabytes, establishing a "Serial sectioning and clearing, 3-dimensional Microscopy, with semi-Automated Reconstruction and Tracing" (SMART) pipeline. This system supports effective connectome-scale mapping of large primates that reveals distinct features of thalamocortical projections of the rhesus monkey brain at the level of individual axonal fibers.

neuroscience↗

bioRxiv2020

Comprehensive genome sequencing analysis as a promising option in the prenatal diagnosis of fetal structural anomalies: a prospective study.

PurposeGenome sequencing (GS) is a powerful tool for postnatal genetic diagnosis, but relevant clinical studies in the field of prenatal diagnosis are few. We aimed to evaluate the feasibility of GS as a first-line approach in prenatal diagnosis and compare its clinical value with the chromosomal microarray analysis (CMA) plus exome sequencing (ES) sequential testing. MethodsWe applied trio GS ([~]40-fold) in parallel with CMA plus ES to investigate the genetic basis for structural or growth anomalies in 111 fetuses and compared their results. ResultsGS covered all genetic variants in 22 diagnosed cases detected by CMA plus ES, yielding a diagnostic rate of 19.8% (22/110). Moreover, GS provided more comprehensive and precise genetic information than CMA plus ES, revealing twin fetuses with an imbalanced translocation arising from a balanced paternal translocation and one fetus with an extra pathogenic variant in the GJA8 gene, and incidentally identified intrauterine CMV infection in a growth-restricted fetus. ConclusionCompared with CMA plus ES, GS offers a more comprehensive view of the genetic etiology of fetal anomalies and provides clues for nongenetic factors such as intrauterine infection. Our study demonstrates the feasibility of GS as a promising first-line test in prenatal diagnosis.

genomics↗

bioRxiv2020

Fitness benefit plays a vital role in the retention of the Pi-ta susceptible alleles

In plants, large numbers of R genes, which segregate as loci with alternative alleles conferring different resistance to pathogens, have been maintained over a long evolutionary time. In theory, there seem to be no reason for hosts to harbor these susceptible alleles in view of their null contribution to resistance. As such, why should populations support disease-susceptible individuals along with disease-resistant individuals? In rice, a single copy R gene Pi-ta segregates for two expressed clades of alleles, one resistant and the other susceptible. We discovered that knockout of the Pi-ta susceptible alleles induced drastic fitness decline in the absence of pathogens. Gene expression profiling and endogenous hormones quantification showed that the susceptible alleles might serve as an off-switch to the downstream immune signaling, thus contributing to fine-tuning of plant defense response. The fitness benefit of carrying a susceptible Pi-ta allele provides a plausible explanation for their retention in the genome.

evolutionary biology↗

bioRxiv2020

Crosstalk between chloroplast protein import and the SUMO system revealed through genetic and molecular investigation

The chloroplast proteome contains thousands of different proteins that are encoded by the nuclear genome. These proteins are imported into the chloroplast via the action of the TOC translocase and associated downstream systems. Our recent work has revealed that the stability of the TOC complex is dynamically regulated by the ubiquitin-dependent chloroplast-associated protein degradation (CHLORAD) pathway. Here, we demonstrate that the stability of the TOC complex is also regulated by the SUMO system. Arabidopsis mutants representing almost the entire SUMO conjugation pathway can partially suppress the phenotype of ppi1, a pale yellow mutant lacking the Toc33 protein. This suppression is linked to the increased stability of TOC proteins and improvements in chloroplast development. In addition, we demonstrate using molecular and biochemical experiments that the SUMO system directly targets TOC proteins. Thus, we have identified a regulatory link between the SUMO system and chloroplast protein import.

cell biology↗

bioRxiv2020

scASK: A novel ensemble framework for classifying cell types based on scRNA-seq data

ABSTRACTThe Human Cell Atlas (HCA) is a large project that aims to identify all cell types in the human body. The dimension reduction and clustering for identification of cell types from single-cell RNA-sequencing (scRNA-seq) data have become foundational approaches to HCA. The major challenges of current computational analyses are of poor performance on large scale data and sensitive to initial data. We present a new ensemble framework called Adaptive Slice KNNs (scASK) to address the challenges for analysing scRNA-seq data with high dimensionality. scASK consists of three innovational modules, called DAS (Data Adaptive Slicing), MCS (Meta Classifiers Selecting) and EMS (Ensemble Mode Switching), respectively, which facilitate scASK to approximate a bias-variance tradeoff beyond classification. Thirteen real scRNA-seq datasets are used to evaluate the performance of scASK. Compared with five popular classification algorithms, our experimental results indicate that scASK achieves the best accuracy and robustness among all competing methods. In conclusion, adaptive slicing is an effective structural reduction procedure, and meanwhile scASK provides novel and robust ensemble framework especially for classifying cell types based on scRNA-seq data. scASK is publically available at https://github.com/liubo2358/scASKcmd.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2020

Intrinsic and extrinsic factors collaborate to activate pharyngeal satellite cells without muscle injury

Satellite cells (SCs), adult muscle stem cells in craniofacial muscles proliferate and differentiate/fuse without injury, unlike quiescent SCs in uninjured limb muscle. However, whether intrinsic or extrinsic factors driving their increased basal activity are largely unknown. We compared SCs from the pharynx, which contains constrictor muscles critical for swallowing, to SCs from limb muscle. Pharyngeal SCs are intrinsically more proliferative and contain higher mitochondrial content relative to limb SCs. Pharyngeal SCs occupy less quiescent microenvironments containing collagen V and pharyngeal muscles provide a distinctive SC niche enriched with neighboring resident macrophages and fibroadipogenic progenitors. Loss of SCs impacts pharyngeal myofiber cross-sectional area and the number of neighboring cells, suggesting that SCs are required to maintain pharyngeal muscle homeostasis and its unique niche. Taken together, this study gives new insights to explain the distinctive SC activity of craniofacial muscles, which may explain their unique susceptibility to various muscular dystrophies.

cell biology↗

bioRxiv2020

MEIS-WNT5A axis regulates development of 4th ventricle choroid plexus

The choroid plexus (ChP) produces cerebrospinal fluid and forms a critical barrier between the brain and the circulation. While the ChP forms in each brain ventricle, it adopts a different shape in each one and remarkably little is known about the mechanisms underlying its development. Here, we show that epithelial WNT5A is critical for determining fourth ventricle (4V) ChP morphogenesis and size. Systemic Wnt5a knockout, or forced WNT5A overexpression beginning at E10.5, profoundly reduced the size and development of ChP in all ventricles. However, conditional deletion of Wnt5a expression in Foxj1-expressing epithelial cells affected only the branched, villous morphology of the 4V ChP. We found that WNT5A was enriched in epithelial cells localized to the distal tips of 4V ChP villi, where WNT5A acted locally to activate non-canonical Wnt signaling via Ror1/Ror2 receptors. During 4V ChP development, MEIS1 bound to the proximal Wnt5a promoter, and gain- and loss-of-function approaches demonstrated that MEIS1 regulated Wnt5a expression. Collectively, our findings demonstrate a dual function of WNT5A in ChP development and identify MEIS1 and MEIS2 as upstream regulators of Wnt5a in the 4V ChP epithelium.

developmental biology↗

bioRxiv2020

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement

Accurate identification of cell types from single-cell RNA sequencing (scRNA-seq) data plays a critical role in a variety of scRNA-seq analysis studies. It corresponds to solving an unsupervised clustering problem, in which the similarity measurement between cells in a high dimensional space affects the result significantly. Although many approaches have been proposed recently, the accuracy of cell type identification still needs to be improved. In this study, we proposed a novel single-cell clustering framework based on similarity learning, called SSRE. In SSRE, we model the relationships between cells based on subspace assumption and generate a sparse representation of the cell-to-cell similarity, which retains the most similar neighbors for each cell. Besides, we adopt classical pairwise similarities incorporated with a gene selection and enhancement strategy to further improve the effectiveness of SSRE. For performance evaluation, we applied SSRE in clustering, visualization, and other exploratory data analysis processes on various scRNA-seq datasets. Experimental results show that SSRE achieves superior performance in most cases compared to several state-of-the-art methods.

bioinformatics↗

bioRxiv2020

Pex24 and Pex32 tether peroxisomes to the ER for organelle biogenesis, positioning and segregation

We analyzed all four Pex23 family proteins of the yeast Hansenula polymorpha, which localize to the ER. Of these Pex24 and Pex32, but not Pex23 and Pex29, accumulate at peroxisome-ER contacts, where they are important for normal peroxisome biogenesis and proliferation and contribute to organelle positioning and segregation. Upon deletion of PEX24 and PEX32 - and to a lesser extent of PEX23 and PEX29 - peroxisome-ER contacts are disrupted, concomitant with peroxisomal defects. These defects are suppressed upon introduction of an artificial peroxisome-ER tether. Accumulation of Pex32 at peroxisomes-ER contacts is lost in the absence of the peroxisomal membrane protein Pex11. At the same time peroxisome-ER contacts are disrupted, indicating that Pex11 contributes to Pex32-dependent peroxisome-ER contact formation. Summarizing, our data indicate that H. polymorpha Pex24 and Pex32 are tethers at peroxisome-ER contacts that are important for normal peroxisome biogenesis and dynamics. SummaryTwo Hansenula polymorpha ER proteins, Pex24 and Pex32, are tethers at peroxisome-ER contacts and function together with the peroxisomal protein Pex11. Their absence disturbs these contacts leading to multiple peroxisomal defects, which can be restored by an artificial tether.

cell biology↗

bioRxiv2020

Two new genetically modified mouse alleles labeling distinct phases of retinal ganglion cell development by fluorescent proteins

During development, retinal progenitor cells (RPCs) take on different trajectories for distinct cell fates. Previous studies have identified key regulators involved in two key steps of retinal ganglion cell (RGC) genesis; Atoh7 functions in a subpopulation of RPCs to render them competent for the RGC fate, whereas Pou4f2 and Isl1 function to specify the RGC fate and promote RGC differentiation. Extensive research has been performed on the roles of these transcription factors in RGC development, but properties of these two phases they represent and the cellular context in which these two factors function have not been thoroughly investigated, largely due to the cellular heterogeneity of developing retina. In this paper, we describe two novel knock-in mouse alleles, Atoh7zsGreenCreERT2 and Pou4f2FlagtdTomato, which enabled us to label retinal cells in the two phases of RGC development by fluorescent proteins. In addition, the Atoh7zsGreenCreERT2 allele also allowed for indirect labeling of RGCs and other cell types upon tamoxifen induction in a dose-dependent manner. Further, these alleles could be used to purify retinal cells of these different phases by fluorescence assisted cell sorting (FACS). Thus, these two alleles can serve as very useful tools for studying the molecular and genetic mechanisms underlying RGC formation.

developmental biology↗